A mother was gunned down in her Queens apartment as her 5-year-old son cowered in another room, and police are questioning the woman’s beau, cops said.

The 29-year-old victim and her son were at their Elmhurst apartment at Justice and 52nd avenues at around 1:50 a.m. when two men, one identified as the woman’s boyfriend, walked in and she was shot twice in the head, police said.

The woman was rushed to Elmhurst Hospital where she was pronounced dead.

Her boyfriend is not believed to be the father of the boy, who was hiding out in another room when his mother was murdered. He was not hurt, cops said.

The identity of the slain woman is being withheld pending family notification, cops said.